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Behrendt U, Burghard V, Wende S, Ulrich K, Wolf J, Neumann-Schaal M, Ulrich A. Schauerella fraxinea gen. nov., sp. nov., a bacterial species that colonises ash trees tolerant to dieback caused by Hymenoscyphus fraxineus. Syst Appl Microbiol 2024; 47:126516. [PMID: 38772267 DOI: 10.1016/j.syapm.2024.126516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/23/2024]
Abstract
The tolerance of ash trees against the pathogen Hymenoscyphus fraxineus seems to be associated with the occurrence of specific microbial taxa on leaves. A group of bacterial isolates, primarily identified on tolerant trees, was investigated with regard to their taxonomic classification and their potential to suppress the ash dieback pathogen. Examination of OGRI values revealed a separate species position. A phylogenomic analysis, based on orthologous and marker genes, indicated a separate genus position along with the species Achromobacter aestuarii. Furthermore, analysis of the ratio of average nucleotide identities and genome alignment fractions demonstrated genomic dissimilarities typically observed for inter-genera comparisons within this family. As a result of these investigations, the strains are considered to represent a separate species within a new genus, for which the name Schauerella fraxinea gen. nov., sp. nov. is proposed, with the type strain B3P038T (=LMG 33092 T = DSM 115926 T). Additionally, a reclassification of the species Achromobacter aestuarii as Schauerella aestuarii comb. nov. is proposed. In a co-cultivation assay, the strains were able to inhibit the growth of a H. fraxineus strain. Accordingly, a functional analysis of the genome of S. fraxinea B3P038T revealed genes mediating the production of antifungal substances. This potential, combined with the prevalent presence in the phyllosphere of tolerant ash trees, makes this group interesting for an inoculation experiment with the aim of controlling the pathogen in an integrative approach. For future field trials, a strain-specific qPCR system was developed to establish an efficient method for monitoring the inoculation success.
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Affiliation(s)
- Undine Behrendt
- Leibniz Center for Agricultural Landscape Research (ZALF), Microbial Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany.
| | - Valentin Burghard
- Leibniz Center for Agricultural Landscape Research (ZALF), Microbial Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany.
| | - Sonja Wende
- Leibniz Center for Agricultural Landscape Research (ZALF), Microbial Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany.
| | - Kristina Ulrich
- Johann Heinrich Von Thünen Institute, Institute of Forest Genetics, Eberswalder Chaussee 3a, 15377 Waldsieversdorf, Germany.
| | - Jacqueline Wolf
- Research Group Bacterial Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
| | - Meina Neumann-Schaal
- Research Group Bacterial Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.
| | - Andreas Ulrich
- Leibniz Center for Agricultural Landscape Research (ZALF), Microbial Biogeochemistry, Eberswalder Str. 84, D-15374 Müncheberg, Germany.
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2
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Battistuzzi M, Morlino MS, Cocola L, Trainotti L, Treu L, Campanaro S, Claudi R, Poletto L, La Rocca N. Transcriptomic and photosynthetic analyses of Synechocystis sp. PCC6803 and Chlorogloeopsis fritschii sp. PCC6912 exposed to an M-dwarf spectrum under an anoxic atmosphere. FRONTIERS IN PLANT SCIENCE 2024; 14:1322052. [PMID: 38304456 PMCID: PMC10830646 DOI: 10.3389/fpls.2023.1322052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 12/29/2023] [Indexed: 02/03/2024]
Abstract
Introduction Cyanobacteria appeared in the anoxic Archean Earth, evolving for the first time oxygenic photosynthesis and deeply changing the atmosphere by introducing oxygen. Starting possibly from UV-protected environments, characterized by low visible and far-red enriched light spectra, cyanobacteria spread everywhere on Earth thanks to their adaptation capabilities in light harvesting. In the last decade, few cyanobacteria species which can acclimate to far-red light through Far-Red Light Photoacclimation (FaRLiP) have been isolated. FaRLiP cyanobacteria were thus proposed as model organisms to study the origin of oxygenic photosynthesis as well as its possible functionality around stars with high far-red emission, the M-dwarfs. These stars are astrobiological targets, as their longevity could sustain life evolution and they demonstrated to host rocky terrestrial-like exoplanets within their Habitable Zone. Methods We studied the acclimation responses of the FaRLiP strain Chlorogloeopsis fritschii sp. PCC6912 and the non-FaRLiP strain Synechocystis sp. PCC6803 to the combination of three simulated light spectra (M-dwarf, solar and far-red) and two atmospheric compositions (oxic, anoxic). We first checked their growth, O2 production and pigment composition, then we studied their transcriptional responses by RNA sequencing under each combination of light spectrum and atmosphere conditions. Results and discussion PCC6803 did not show relevant differences in gene expression when comparing the responses to M-dwarf and solar-simulated lights, while far-red caused a variation in the transcriptional level of many genes. PCC6912 showed, on the contrary, different transcriptional responses to each light condition and activated the FaRLiP response under the M-dwarf simulated light. Surprisingly, the anoxic atmosphere did not impact the transcriptional profile of the 2 strains significantly. Results show that both cyanobacteria seem inherently prepared for anoxia and to harvest the photons emitted by a simulated M-dwarf star, whether they are only visible (PCC6803) or also far-red photons (PCC6912). They also show that visible photons in the simulated M-dwarf are sufficient to keep a similar metabolism with respect to solar-simulated light. Conclusion Results prove the adaptability of the cyanobacterial metabolism and enhance the plausibility of finding oxygenic biospheres on exoplanets orbiting M-dwarf stars.
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Affiliation(s)
- Mariano Battistuzzi
- National Council of Research of Italy, Institute for Photonics and Nanotechnologies (CNR-IFN), Padua, Italy
- Department of Biology, University of Padua, Padua, Italy
- Center for Space Studies and Activities (CISAS), University of Padua, Padua, Italy
| | | | - Lorenzo Cocola
- National Council of Research of Italy, Institute for Photonics and Nanotechnologies (CNR-IFN), Padua, Italy
| | | | - Laura Treu
- Department of Biology, University of Padua, Padua, Italy
| | | | - Riccardo Claudi
- National Institute for Astrophysics, Astronomical Observatory of Padua (INAF-OAPD), Padua, Italy
- Department of Mathematics and Physics, University Roma Tre, Rome, Italy
| | - Luca Poletto
- National Council of Research of Italy, Institute for Photonics and Nanotechnologies (CNR-IFN), Padua, Italy
| | - Nicoletta La Rocca
- Department of Biology, University of Padua, Padua, Italy
- Center for Space Studies and Activities (CISAS), University of Padua, Padua, Italy
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3
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Kumar G, Kallscheuer N, Jogler M, Wiegand S, Heuer A, Boedeker C, Rohde M, Jogler C. Stratiformator vulcanicus gen. nov., sp. nov., a marine member of the family Planctomycetaceae isolated from a red biofilm in the Tyrrhenian Sea close to the volcanic island Panarea. Antonie Van Leeuwenhoek 2023; 116:995-1007. [PMID: 37584762 PMCID: PMC10509075 DOI: 10.1007/s10482-023-01860-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/21/2023] [Indexed: 08/17/2023]
Abstract
A novel planctomycetal strain, designated Pan189T, was isolated from biofilm material sampled close to Panarea Island in the Tyrrhenian Sea. Cells of strain Pan189T are round grain rice-shaped, form pink colonies and display typical planctomycetal characteristics including asymmetric cell division through polar budding and presence of crateriform structures. Cells bear a stalk opposite to the division pole and fimbriae cover the cell surface. Strain Pan189T has a mesophilic (optimum at 24 °C) and neutrophilic (optimum at pH 7.5) growth profile, is aerobic and heterotrophic. Under laboratory-scale cultivation conditions, it reached a generation time of 102 h (µmax = 0.0068 h-1), which places the strain among the slowest growing members of the phylum Planctomycetota characterized so far. The genome size of the strain is with 5.23 Mb at the lower limit among the family Planctomycetaceae (5.1-8.9 Mb). Phylogenetically, the strain represents a novel genus and species in the family Planctomycetaceae, order Planctomycetales, class Planctomycetia. We propose the name Stratiformator vulcanicus gen. nov., sp. nov. for the novel taxon, that is represented by the type strain Pan189T (= DSM 101711 T = CECT 30699 T).
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Affiliation(s)
- Gaurav Kumar
- Department of Microbial Interactions, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany
| | - Nicolai Kallscheuer
- Department of Microbial Interactions, Friedrich Schiller University, Jena, Germany
| | - Mareike Jogler
- Department of Microbial Interactions, Friedrich Schiller University, Jena, Germany
| | - Sandra Wiegand
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Anja Heuer
- Leibniz Institute DSMZ, Brunswick, Germany
| | | | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Brunswick, Germany
| | - Christian Jogler
- Department of Microbial Interactions, Friedrich Schiller University, Jena, Germany.
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany.
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4
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Methner A, Kuzyk SB, Petersen J, Bauer S, Brinkmann H, Sichau K, Wanner G, Wolf J, Neumann-Schaal M, Henke P, Tank M, Spröer C, Bunk B, Overmann J. Thiorhodovibrio frisius and Trv. litoralis spp. nov., Two Novel Members from a Clade of Fastidious Purple Sulfur Bacteria That Exhibit Unique Red-Shifted Light-Harvesting Capabilities. Microorganisms 2023; 11:2394. [PMID: 37894052 PMCID: PMC10609205 DOI: 10.3390/microorganisms11102394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/21/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
In the pursuit of cultivating anaerobic anoxygenic phototrophs with unusual absorbance spectra, a purple sulfur bacterium was isolated from the shoreline of Baltrum, a North Sea island of Germany. It was designated strain 970, due to a predominant light harvesting complex (LH) absorption maximum at 963-966 nm, which represents the furthest infrared-shift documented for such complexes containing bacteriochlorophyll a. A polyphasic approach to bacterial systematics was performed, comparing genomic, biochemical, and physiological properties. Strain 970 is related to Thiorhodovibrio winogradskyi DSM 6702T by 26.5, 81.9, and 98.0% similarity via dDDH, ANI, and 16S rRNA gene comparisons, respectively. The photosynthetic properties of strain 970 were unlike other Thiorhodovibrio spp., which contained typical LH absorbing characteristics of 800-870 nm, as well as a newly discovered absorption band at 908 nm. Strain 970 also had a different photosynthetic operon composition. Upon genomic comparisons with the original Thiorhodovibrio strains DSM 6702T and strain 06511, the latter was found to be divergent, with 25.3, 79.1, and 97.5% similarity via dDDH, ANI, and 16S rRNA gene homology to Trv. winogradskyi, respectively. Strain 06511 (=DSM 116345T) is thereby described as Thiorhodovibrio litoralis sp. nov., and the unique strain 970 (=DSM 111777T) as Thiorhodovibrio frisius sp. nov.
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Affiliation(s)
- Anika Methner
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Steven B Kuzyk
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Jörn Petersen
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Sabine Bauer
- Former Institution: Paläomikrobiologie, Institut für Chemie und Biologie des Meeres, Universität Oldenburg, Postfach 2503, 26111 Oldenburg, Germany
| | - Henner Brinkmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Katja Sichau
- Bereich Mikrobiologie, Department Biologie I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Gerhard Wanner
- Bereich Mikrobiologie, Department Biologie I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Jacqueline Wolf
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Petra Henke
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Marcus Tank
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Boyke Bunk
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Jörg Overmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
- Former Institution: Paläomikrobiologie, Institut für Chemie und Biologie des Meeres, Universität Oldenburg, Postfach 2503, 26111 Oldenburg, Germany
- Bereich Mikrobiologie, Department Biologie I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
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5
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Han M, Schierstaedt J, Duan Y, Nietschke M, Jechalke S, Wolf J, Hensel M, Neumann-Schaal M, Schikora A. Salmonella enterica relies on carbon metabolism to adapt to agricultural environments. Front Microbiol 2023; 14:1213016. [PMID: 37744895 PMCID: PMC10513388 DOI: 10.3389/fmicb.2023.1213016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/11/2023] [Indexed: 09/26/2023] Open
Abstract
Salmonella enterica, a foodborne and human pathogen, is a constant threat to human health. Agricultural environments, for example, soil and plants, can be ecological niches and vectors for Salmonella transmission. Salmonella persistence in such environments increases the risk for consumers. Therefore, it is necessary to investigate the mechanisms used by Salmonella to adapt to agricultural environments. We assessed the adaptation strategy of S. enterica serovar Typhimurium strain 14028s to agricultural-relevant situations by analyzing the abundance of intermediates in glycolysis and the tricarboxylic acid pathway in tested environments (diluvial sand soil suspension and leaf-based media from tomato and lettuce), as well as in bacterial cells grown in such conditions. By reanalyzing the transcriptome data of Salmonella grown in those environments and using an independent RT-qPCR approach for verification, several genes were identified as important for persistence in root or leaf tissues, including the pyruvate dehydrogenase subunit E1 encoding gene aceE. In vivo persistence assay in tomato leaves confirmed the crucial role of aceE. A mutant in another tomato leaf persistence-related gene, aceB, encoding malate synthase A, displayed opposite persistence features. By comparing the metabolites and gene expression of the wild-type strain and its aceB mutant, fumarate accumulation was discovered as a potential way to replenish the effects of the aceB mutation. Our research interprets the mechanism of S. enterica adaptation to agriculture by adapting its carbon metabolism to the carbon sources available in the environment. These insights may assist in the development of strategies aimed at diminishing Salmonella persistence in food production systems.
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Affiliation(s)
- Min Han
- Federal Research Centre for Cultivated Plants, Julius Kühn Institute (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Jasper Schierstaedt
- Federal Research Centre for Cultivated Plants, Julius Kühn Institute (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
- Department Plant-Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Großbeeren, Germany
| | - Yongming Duan
- Federal Research Centre for Cultivated Plants, Julius Kühn Institute (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Monika Nietschke
- Division of Microbiology, Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Sven Jechalke
- Institute of Phytopathology, Research Centre for Biosystems, Land Use and Nutrition (IFZ), Justus-Liebig-University Gießen, Gießen, Germany
| | - Jacqueline Wolf
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Michael Hensel
- Division of Microbiology, Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Adam Schikora
- Federal Research Centre for Cultivated Plants, Julius Kühn Institute (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
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6
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Bublitz A, Brauer M, Wagner S, Hofer W, Müsken M, Deschner F, Lesker TR, Neumann-Schaal M, Paul LS, Nübel U, Bartel J, Kany AM, Zühlke D, Bernecker S, Jansen R, Sievers S, Riedel K, Herrmann J, Müller R, Fuchs TM, Strowig T. The natural product chlorotonil A preserves colonization resistance and prevents relapsing Clostridioides difficile infection. Cell Host Microbe 2023; 31:734-750.e8. [PMID: 37098342 DOI: 10.1016/j.chom.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 02/24/2023] [Accepted: 04/03/2023] [Indexed: 04/27/2023]
Abstract
Clostridioides difficile infections (CDIs) remain a healthcare problem due to high rates of relapsing/recurrent CDIs (rCDIs). Breakdown of colonization resistance promoted by broad-spectrum antibiotics and the persistence of spores contribute to rCDI. Here, we demonstrate antimicrobial activity of the natural product class of chlorotonils against C. difficile. In contrast to vancomycin, chlorotonil A (ChA) efficiently inhibits disease and prevents rCDI in mice. Notably, ChA affects the murine and porcine microbiota to a lesser extent than vancomycin, largely preserving microbiota composition and minimally impacting the intestinal metabolome. Correspondingly, ChA treatment does not break colonization resistance against C. difficile and is linked to faster recovery of the microbiota after CDI. Additionally, ChA accumulates in the spore and inhibits outgrowth of C. difficile spores, thus potentially contributing to lower rates of rCDI. We conclude that chlorotonils have unique antimicrobial properties targeting critical steps in the infection cycle of C. difficile.
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Affiliation(s)
- Arne Bublitz
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Madita Brauer
- Institute of Microbiology, Department of Microbial Physiology and Molecular Biology, University of Greifswald, Greifswald, Germany; Institute of Marine Biotechnology e.V., Greifswald, Germany
| | - Stefanie Wagner
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
| | - Walter Hofer
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany; Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Mathias Müsken
- Central Facility for Microscopy, Helmholtz Center for Infection Research (HZI), Braunschweig, Germany
| | - Felix Deschner
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany; Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Till R Lesker
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Bacterial Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; Braunschweig Integrated Center of Systems Biology (BRICS), Technical University, Braunschweig, Germany
| | - Lena-Sophie Paul
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
| | - Ulrich Nübel
- Braunschweig Integrated Center of Systems Biology (BRICS), Technical University, Braunschweig, Germany; Microbial Genome Research, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Jürgen Bartel
- Institute of Microbiology, Department of Microbial Proteomics, University of Greifswald, Greifswald, Germany
| | - Andreas M Kany
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany; Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Daniela Zühlke
- Institute of Microbiology, Department of Microbial Physiology and Molecular Biology, University of Greifswald, Greifswald, Germany
| | - Steffen Bernecker
- Department of Microbial Drugs, Helmholtz Center for Infection Research (HZI), Braunschweig, Germany
| | - Rolf Jansen
- Department of Microbial Drugs, Helmholtz Center for Infection Research (HZI), Braunschweig, Germany
| | - Susanne Sievers
- Institute of Microbiology, Department of Microbial Physiology and Molecular Biology, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, Department of Microbial Physiology and Molecular Biology, University of Greifswald, Greifswald, Germany; Institute of Marine Biotechnology e.V., Greifswald, Germany
| | - Jennifer Herrmann
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany; Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany; Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Thilo M Fuchs
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany.
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany; Centre for Individualised Infection Medicine (CiiM), Hannover, Germany.
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7
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Bachhar A, Jablonsky J. Entner-Doudoroff pathway in Synechocystis PCC 6803: Proposed regulatory roles and enzyme multifunctionalities. Front Microbiol 2022; 13:967545. [PMID: 36051759 PMCID: PMC9424857 DOI: 10.3389/fmicb.2022.967545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
The Entner-Doudoroff pathway (ED-P) was established in 2016 as the fourth glycolytic pathway in Synechocystis sp. PCC 6803. ED-P consists of two reactions, the first catalyzed by 6-phosphogluconate dehydratase (EDD), the second by keto3-deoxygluconate-6-phosphate aldolase/4-hydroxy-2-oxoglutarate aldolase (EDA). ED-P was previously concluded to be a widespread (∼92%) pathway among cyanobacteria, but current bioinformatic analysis estimated the occurrence of ED-P to be either scarce (∼1%) or uncommon (∼47%), depending if dihydroxy-acid dehydratase (ilvD) also functions as EDD (currently assumed). Thus, the biochemical characterization of ilvD is a task pending to resolve this uncertainty. Next, we have provided new insights into several single and double glycolytic mutants based on kinetic model of central carbon metabolism of Synechocystis. The model predicted that silencing 6-phosphogluconate dehydrogenase (gnd) could be coupled with ∼90% down-regulation of G6P-dehydrogenase, also limiting the metabolic flux via ED-P. Furthermore, our metabolic flux estimation implied that growth impairment linked to silenced EDA under mixotrophic conditions is not caused by diminished carbon flux via ED-P but rather by a missing mechanism related to the role of EDA in metabolism. We proposed two possible, mutually non-exclusive explanations: (i) Δeda leads to disrupted carbon catabolite repression, regulated by 2-keto3-deoxygluconate-6-phosphate (ED-P intermediate), and (ii) EDA catalyzes the interconversion between glyoxylate and 4-hydroxy-2-oxoglutarate + pyruvate in the proximity of TCA cycle, possibly effecting the levels of 2-oxoglutarate under Δeda. We have also proposed a new pathway from EDA toward proline, which could explain the proline accumulation under Δeda. In addition, the presented in silico method provides an alternative to 13C metabolic flux analysis for marginal metabolic pathways around/below the threshold of ultrasensitive LC-MS. Finally, our in silico analysis provided alternative explanations for the role of ED-P in Synechocystis while identifying some severe uncertainties.
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8
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Lopez Marin MA, Suman J, Jani K, Ulbrich P, Cajthaml T, Pajer P, Wolf J, Neumann-Schaal M, Strejcek M, Uhlik O. Pedomonas mirosovicensis gen. nov., sp. nov., a bacterium isolated from soil with the aid of Micrococcus luteus culture supernatant containing resuscitation-promoting factor. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An orange-golden iridescent culture, designated A1X5R2T, was isolated from a compost soil suspension which was amended with
Micrococcus luteus
NCTC 2665T culture supernatant. The cells were non-motile, Gram-stain-negative, 0.4–0.5 µm wide and 0.7–1.4 µm long. The 16S rRNA-based phylogenetic and whole-genome analyses revealed that strain A1X5R2T forms a distinct lineage within the family
Sphingosinicellaceae
and is closely related to members of the genus
Sphingoaurantiacus
(
S. capsulatus
, 93.04 % similarity, and
S. polygranulatus
, 92.77 %). The organism grew at 22–47 °C (optimal at 37 °C), salinity <3 % (optimal at 1.5 %) and at pH 7. The major respiratory quinone was ubiquinone-10, but a small quantity of ubiquinone-9 was also detected The major polyamine was homospermidine, but a small quantity of putrescine was also detected. The strain contained C18 : 1ω7c, C16 : 0, C16 : 1 ω7c and C18 : 0 as the major fatty acids. The main polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, sphingoglycolipid, diphosphatidylglycerol, two unidentified phospholipids and three unidentified amino lipids. The DNA G+C content was 64.9 mol%. According to the results of phylogenetic and phylogenomic analyses, as well as its physiological characteristics, strain A2X5R2T represents the type species of a novel genus within the family
Sphingosinicellaceae
. The name Pedomonas mirosovicensis gen. nov., sp. nov. is proposed, with the type strain being A1X5R2T (=NCCB 100839T=DSM 112829T).
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Affiliation(s)
- Marco A. Lopez Marin
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technicka 3, 16628 Prague, Czech Republic
| | - Jachym Suman
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technicka 3, 16628 Prague, Czech Republic
| | - Kunal Jani
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technicka 3, 16628 Prague, Czech Republic
| | - Pavel Ulbrich
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technicka 3, 16628 Prague, Czech Republic
| | - Tomas Cajthaml
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220, Prague, Czech Republic
| | - Petr Pajer
- Military Health Institute, Ministry of Defence of the Czech Republic, U Vojenske nemocnice 1200, 169 02, Prague, Czech Republic
| | - Jacqueline Wolf
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstr. 7 B, 38124, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstr. 7 B, 38124, Braunschweig, Germany
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technicka 3, 16628 Prague, Czech Republic
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technicka 3, 16628 Prague, Czech Republic
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9
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A Ubiquitously Conserved Cyanobacterial Protein Phosphatase Essential for High Light Tolerance in a Fast-Growing Cyanobacterium. Microbiol Spectr 2022; 10:e0100822. [PMID: 35727069 PMCID: PMC9430166 DOI: 10.1128/spectrum.01008-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Synechococcus elongatus UTEX 2973, the fastest-growing cyanobacterial strain known, optimally grows under extreme high light (HL) intensities of 1,500-2,500 μmol photons m-2 s-1, which is lethal to most other photosynthetic microbes. We leveraged the few genetic differences between Synechococcus 2973 and the HL sensitive strain Synechococcus elongatus PCC 7942 to unravel factors essential for the high light tolerance. We identified a novel protein in Synechococcus 2973 that we have termed HltA for High light tolerance protein A. Using bioinformatic tools, we determined that HltA contains a functional PP2C-type protein phosphatase domain. Phylogenetic analysis showed that the PP2C domain belongs to the bacterial-specific Group II family and is closely related to the environmental stress response phosphatase RsbU. Additionally, we showed that unlike any previously described phosphatases, HltA contains a single N-terminal regulatory GAF domain. We found hltA to be ubiquitous throughout cyanobacteria, indicative of its potentially important role in the photosynthetic lifestyle of these oxygenic phototrophs. Mutations in the hltA gene resulted in severe defects specific to high light growth. These results provide evidence that hltA is a key factor in the tolerance of Synechococcus 2973 to high light and will open new insights into the mechanisms of cyanobacterial light stress response. IMPORTANCE Cyanobacteria are a diverse group of photosynthetic prokaryotes. The cyanobacterium Synechococcus 2973 is a high light tolerant strain with industrial promise due to its fast growth under high light conditions and the availability of genetic modification tools. Currently, little is known about the high light tolerance mechanisms of Synechococcus 2973, and there are many unknowns overall regarding high light tolerance of cyanobacteria. In this study, a comparative genomic analysis of Synechococcus 2973 identified a single nucleotide polymorphism in a locus encoding a serine phosphatase as a key factor for high light tolerance. This novel GAF-containing phosphatase was found to be the sole Group II metal-dependent protein phosphatase that is evolutionarily conserved throughout cyanobacteria. These results shed new light on the light response mechanisms of Synechococcus 2973, improving our understanding of environmental stress response. Additionally, this work will help facilitate the development of Synechococcus 2973 as an industrially useful organism.
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10
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Spring S, Rohde M, Bunk B, Spröer C, Will SE, Neumann-Schaal M. New insights into the energy metabolism and taxonomy of Deferribacteres revealed by the characterization of a new isolate from a hypersaline microbial mat. Environ Microbiol 2022; 24:2543-2575. [PMID: 35415868 DOI: 10.1111/1462-2920.15999] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/04/2022] [Indexed: 12/13/2022]
Abstract
Strain L21-Ace-BEST , isolated from a lithifying cyanobacterial mat, could be assigned to a novel species and genus within the Deferribacteres. It is an important model organism for the study of anaerobic acetate degradation under hypersaline conditions. The metabolism of strain L21-Ace-BEST was characterized by biochemical studies, comparative genome analyses, and the evaluation of gene expression patterns. The central metabolic pathway is the citric acid cycle, which is mainly controlled by the enzyme succinyl-CoA:acetate-CoA transferase. The potential use of a reversed oxidative citric acid cycle to fix CO2 has been revealed through genome analysis. However, no autotrophic growth was detected in this strain, whereas sulfide and H2 can be used mixotrophically. Preferred electron acceptors for the anaerobic oxidation of acetate are nitrate, fumarate and DMSO, while oxygen can be utilized only under microoxic conditions. Aerotolerant growth by fermentation was observed at higher oxygen concentrations. The redox cycling of sulfur/sulfide enables the generation of reducing power for the assimilation of acetate during growth and could prevent the over-reduction of cells in stationary phase. Extracellular electron transfer appears to be an essential component of the respiratory metabolism in this clade of Deferribacteres and may be involved in the reduction of nitrite to ammonium. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Stefan Spring
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, HZI, Braunschweig, Germany
| | - Boyke Bunk
- Department Bioinformatics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Department Bioinformatics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine Eva Will
- Research Group Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Research Group Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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11
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Michel AM, Borrero-de Acuña JM, Molinari G, Ünal CM, Will S, Derksen E, Barthels S, Bartram W, Schrader M, Rohde M, Zhang H, Hoffmann T, Neumann-Schaal M, Bremer E, Jahn D. Cellular adaptation of Clostridioides difficile to high salinity encompasses a compatible solute-responsive change in cell morphology. Environ Microbiol 2022; 24:1499-1517. [PMID: 35106888 DOI: 10.1111/1462-2920.15925] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 11/27/2022]
Abstract
Infections by the pathogenic gut bacterium Clostridioides difficile cause severe diarrheas up to a toxic megacolon and are currently among the major causes of lethal bacterial infections. Successful bacterial propagation in the gut is strongly associated with the adaptation to changing nutrition-caused environmental conditions; e.g. environmental salt stresses. Concentrations of 350 mM NaCl, the prevailing salinity in the colon, led to significantly reduced growth of C. difficile. Metabolomics of salt- stressed bacteria revealed a major reduction of the central energy generation pathways, including the Stickland-fermentation reactions. No obvious synthesis of compatible solutes was observed up to 24 h of growth. The ensuing limited tolerance to high salinity and absence of compatible solute synthesis might result from an evolutionary adaptation to the exclusive life of C. difficile in the mammalian gut. Addition of the compatible solutes carnitine, glycine-betaine, γ-butyrobetaine, crotonobetaine, homobetaine, proline-betaine and dimethylsulfoniopropionate (DMSP) restored growth (choline and proline failed) under conditions of high salinity. A bioinformatically-identified OpuF-type ABC-transporter imported most of the used compatible solutes. A long-term adaptation after 48 h included a shift of the Stickland fermentation-based energy metabolism from the utilization to the accumulation of L-proline and resulted in restored growth. Surprisingly, salt stress resulted in the formation of coccoid C. difficile cells instead of the typical rod-shaped cells, a process reverted by the addition of several compatible solutes. Hence, compatible solute import via OpuF is the major immediate adaptation strategy of C. difficile to high salinity-incurred cellular stress. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Annika-Marisa Michel
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - José Manuel Borrero-de Acuña
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.,Universidad de Sevilla, Facultad de Biología, Departamento de Microbiología, Av. de la Reina Mercedes, n° 6, CP, 41012, Sevilla, Spain
| | - Gabriella Molinari
- Central Facility for Microscopy, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Can Murat Ünal
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Sabine Will
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Elisabeth Derksen
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Stefan Barthels
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Wiebke Bartram
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Michel Schrader
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Hao Zhang
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.,School of Life Science and Technology, Changchun University of Science and Technology, No. 7186 Weixing Road, 130022, Changchun, China
| | - Tamara Hoffmann
- Laboratory for Microbiology, Department of Biology, Philipps-Universität Marburg, Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
| | - Meina Neumann-Schaal
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.,Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-Universität Marburg, Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
| | - Dieter Jahn
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
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12
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Proteogenomic Analysis Provides Novel Insight into Genome Annotation and Nitrogen Metabolism in Nostoc sp. PCC 7120. Microbiol Spectr 2021; 9:e0049021. [PMID: 34523988 PMCID: PMC8557916 DOI: 10.1128/spectrum.00490-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Cyanobacteria, capable of oxygenic photosynthesis, play a vital role in nitrogen and carbon cycles. Nostoc sp. PCC 7120 (Nostoc 7120) is a model cyanobacterium commonly used to study cell differentiation and nitrogen metabolism. Although its genome was released in 2002, a high-quality genome annotation remains unavailable for this model cyanobacterium. Therefore, in this study, we performed an in-depth proteogenomic analysis based on high-resolution mass spectrometry (MS) data to refine the genome annotation of Nostoc 7120. We unambiguously identified 5,519 predicted protein-coding genes and revealed 26 novel genes, 75 revised genes, and 27 different kinds of posttranslational modifications in Nostoc 7120. A subset of these novel proteins were further validated at both the mRNA and peptide levels. Functional analysis suggested that many newly annotated proteins may participate in nitrogen or cadmium/mercury metabolism in Nostoc 7120. Moreover, we constructed an updated Nostoc 7120 database based on our proteogenomic results and presented examples of how the updated database could be used to improve the annotation of proteomic data. Our study provides the most comprehensive annotation of the Nostoc 7120 genome thus far and will serve as a valuable resource for the study of nitrogen metabolism in Nostoc 7120. IMPORTANCE Cyanobacteria are a large group of prokaryotes capable of oxygenic photosynthesis and play a vital role in nitrogen and carbon cycles on Earth. Nostoc 7120 is a commonly used model cyanobacterium for studying cell differentiation and nitrogen metabolism. In this study, we presented the first comprehensive draft map of the Nostoc 7120 proteome and a wide range of posttranslational modifications. In addition, we constructed an updated database of Nostoc 7120 based on our proteogenomic results and presented examples of how the updated database could be used for system-level studies of Nostoc 7120. Our study provides the most comprehensive annotation of Nostoc 7120 genome and a valuable resource for the study of nitrogen metabolism in this model cyanobacterium.
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13
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Roca M, Pérez-Gálvez A. Metabolomics of Chlorophylls and Carotenoids: Analytical Methods and Metabolome-Based Studies. Antioxidants (Basel) 2021; 10:1622. [PMID: 34679756 PMCID: PMC8533378 DOI: 10.3390/antiox10101622] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/03/2021] [Accepted: 10/12/2021] [Indexed: 01/27/2023] Open
Abstract
Chlorophylls and carotenoids are two families of antioxidants present in daily ingested foods, whose recognition as added-value ingredients runs in parallel with the increasing number of demonstrated functional properties. Both groups include a complex and vast number of compounds, and extraction and analysis methods evolved recently to a modern protocol. New methodologies are more potent, precise, and accurate, but their application requires a better understanding of the technical and biological context. Therefore, the present review compiles the basic knowledge and recent advances of the metabolomics of chlorophylls and carotenoids, including the interrelation with the primary metabolism. The study includes material preparation and extraction protocols, the instrumental techniques for the acquisition of spectroscopic and spectrometric properties, the workflows and software tools for data pre-processing and analysis, and the application of mass spectrometry to pigment metabolomics. In addition, the review encompasses a critical description of studies where metabolomics analyses of chlorophylls and carotenoids were developed as an approach to analyzing the effects of biotic and abiotic stressors on living organisms.
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Affiliation(s)
| | - Antonio Pérez-Gálvez
- Food Phytochemistry Department, Instituto de la Grasa (CSIC), Building 46, 41013 Sevilla, Spain;
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14
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Abstract
Species of the floating, freshwater fern Azolla form a well-characterized symbiotic association with the non-culturable cyanobacterium Nostoc azollae, which fixes nitrogen for the plant. However, several cyanobacterial strains have over the years been isolated and cultured from Azolla from all over the world. The genomes of 10 of these strains were sequenced and compared with each other, with other symbiotic cyanobacterial strains, and with similar strains that were not isolated from a symbiotic association. The 10 strains fell into three distinct groups: six strains were nearly identical to the non-symbiotic strain, Nostoc (Anabaena) variabilis ATCC 29413; three were similar to the symbiotic strain, Nostoc punctiforme, and one, Nostoc sp. 2RC, was most similar to non-symbiotic strains of Nostoc linckia. However, Nostoc sp. 2RC was unusual because it has three sets of nitrogenase genes; it has complete gene clusters for two distinct Mo-nitrogenases and an alternative V-nitrogenase. Genes for Mo-nitrogenase, sugar transport, chemotaxis and pili characterized all the symbiotic strains. Several of the strains infected the liverwort Blasia, including N. variabilis ATCC 29413, which did not originate from Azolla but rather from a sewage pond. However, only Nostoc sp. 2RC, which produced highly motile hormogonia, was capable of high-frequency infection of Blasia. Thus, some of these strains, which grow readily in the laboratory, may be useful in establishing novel symbiotic associations with other plants.
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Affiliation(s)
- Brenda S. Pratte
- Department of Biology, University of Missouri–St. Louis, One University Blvd, St. Louis, MO 63121, USA
| | - Teresa Thiel
- Department of Biology, University of Missouri–St. Louis, One University Blvd, St. Louis, MO 63121, USA
- *Correspondence: Teresa Thiel,
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15
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Particulate Metabolites and Transcripts Reflect Diel Oscillations of Microbial Activity in the Surface Ocean. mSystems 2021; 6:6/3/e00896-20. [PMID: 33947808 PMCID: PMC8269247 DOI: 10.1128/msystems.00896-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Light fuels photosynthesis and organic matter production by primary producers in the sunlit ocean. The quantity and quality of the organic matter produced influence community function, yet in situ measurements of metabolites, the products of cellular metabolism, over the diel cycle are lacking. We evaluated community-level biochemical consequences of oscillations of light in the North Pacific Subtropical Gyre by quantifying 79 metabolites in particulate organic matter from 15 m every 4 h over 8 days. Total particulate metabolite concentration peaked at dusk and represented up to 2% of total particulate organic carbon (POC). The concentrations of 55/79 (70%) individual metabolites exhibited significant 24-h periodicity, with daily fold changes from 1.6 to 12.8, often greater than those of POC and flow cytometry-resolvable biomass, which ranged from 1.2 to 2.8. Paired metatranscriptome analysis revealed the taxa involved in production and consumption of a subset of metabolites. Primary metabolites involved in anabolism and redox maintenance had significant 24-h periodicity and diverse organisms exhibited diel periodicity in transcript abundance associated with these metabolites. Compounds with osmotic properties displayed the largest oscillations in concentration, implying rapid turnover and supporting prior evidence of functions beyond cell turgor maintenance. The large daily oscillation of trehalose paired with metatranscriptome and culture data showed that trehalose is produced by the nitrogen-fixing cyanobacterium Crocosphaera, likely to store energy for nighttime metabolism. Together, paired measurements of particulate metabolites and transcripts resolve strategies that microbes use to manage daily energy and redox oscillations and highlight dynamic metabolites with cryptic roles in marine microbial ecosystems.IMPORTANCE Fueled by light, phytoplankton produce the organic matter that supports ocean ecosystems and carbon sequestration. Ocean change impacts microbial metabolism with repercussions for biogeochemical cycling. As the small molecule products of cellular metabolism, metabolites often change rapidly in response to environmental conditions and form the basis of energy and nutrient management and storage within cells. By pairing measurements of metabolites and gene expression in the stratified surface ocean, we reveal strategies of microbial energy management over the day-night cycle and hypothesize that oscillating metabolites are important substrates for dark respiration by phytoplankton. These high-resolution diel measurements of in situ metabolite concentrations form the basis for future work into the specific roles these compounds play in marine microbial communities.
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16
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Khoiri AN, Cheevadhanarak S, Jirakkakul J, Dulsawat S, Prommeenate P, Tachaleat A, Kusonmano K, Wattanachaisaereekul S, Sutheeworapong S. Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management. Front Microbiol 2021; 12:623799. [PMID: 33828538 PMCID: PMC8019924 DOI: 10.3389/fmicb.2021.623799] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/01/2021] [Indexed: 12/21/2022] Open
Abstract
Converting conventional farms to organic systems to improve ecosystem health is an emerging trend in recent decades, yet little is explored to what extent and how this process drives the taxonomic diversity and functional capacity of above-ground microbes. This study was, therefore, conducted to investigate the effects of agricultural management, i.e., organic, transition, and conventional, on the structure and function of sugarcane phyllosphere microbial community using the shotgun metagenomics approach. Comparative metagenome analysis exhibited that farming practices strongly influenced taxonomic and functional diversities, as well as co-occurrence interactions of phyllosphere microbes. A complex microbial network with the highest connectivity was observed in organic farming, indicating strong resilient capabilities of its microbial community to cope with the dynamic environmental stressors. Organic farming also harbored genus Streptomyces as the potential keystone species and plant growth-promoting bacteria as microbial signatures, including Mesorhizobium loti, Bradyrhizobium sp. SG09, Lactobacillus plantarum, and Bacillus cellulosilyticus. Interestingly, numerous toxic compound-degrading species were specifically enriched in transition farming, which might suggest their essential roles in the transformation of conventional to organic farming. Moreover, conventional practice diminished the abundance of genes related to cell motility and energy metabolism of phyllosphere microbes, which could negatively contribute to lower microbial diversity in this habitat. Altogether, our results demonstrated the response of sugarcane-associated phyllosphere microbiota to specific agricultural managements that played vital roles in sustainable sugarcane production.
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Affiliation(s)
- Ahmad Nuruddin Khoiri
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Supapon Cheevadhanarak
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Jiraporn Jirakkakul
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Sudarat Dulsawat
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Peerada Prommeenate
- Biochemical Engineering and Systems Biology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Anuwat Tachaleat
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Kanthida Kusonmano
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Songsak Wattanachaisaereekul
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Faculty of Food Industry, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Sawannee Sutheeworapong
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
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17
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Filling the Gaps in the Cyanobacterial Tree of Life-Metagenome Analysis of Stigonema ocellatum DSM 106950, Chlorogloea purpurea SAG 13.99 and Gomphosphaeria aponina DSM 107014. Genes (Basel) 2021; 12:genes12030389. [PMID: 33803228 PMCID: PMC8001431 DOI: 10.3390/genes12030389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/18/2021] [Accepted: 03/03/2021] [Indexed: 12/26/2022] Open
Abstract
Cyanobacteria represent one of the most important and diverse lineages of prokaryotes with an unparalleled morphological diversity ranging from unicellular cocci and characteristic colony-formers to multicellular filamentous strains with different cell types. Sequencing of more than 1200 available reference genomes was mainly driven by their ecological relevance (Prochlorococcus, Synechococcus), toxicity (Microcystis) and the availability of axenic strains. In the current study three slowly growing non-axenic cyanobacteria with a distant phylogenetic positioning were selected for metagenome sequencing in order to (i) investigate their genomes and to (ii) uncover the diversity of associated heterotrophs. High-throughput Illumina sequencing, metagenomic assembly and binning allowed us to establish nearly complete high-quality draft genomes of all three cyanobacteria and to determine their phylogenetic position. The cyanosphere of the limnic isolates comprises up to 40 heterotrophic bacteria that likely coexisted for several decades, and it is dominated by Alphaproteobacteria and Bacteriodetes. The diagnostic marker protein RpoB ensured in combination with our novel taxonomic assessment via BLASTN-dependent text-mining a reliable classification of the metagenome assembled genomes (MAGs). The detection of one new family and more than a dozen genera of uncultivated heterotrophic bacteria illustrates that non-axenic cyanobacteria are treasure troves of hidden microbial diversity.
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18
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Satjarak A, Graham LE, Piotrowski MJ, Trest MT, Wilcox LW, Cook ME, Knack JJ, Arancibia-Avila P. Shotgun metagenomics and microscopy indicate diverse cyanophytes, other bacteria, and microeukaryotes in the epimicrobiota of a northern Chilean wetland Nostoc (Cyanobacteria). JOURNAL OF PHYCOLOGY 2021; 57:39-50. [PMID: 33070358 DOI: 10.1111/jpy.13084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 09/01/2020] [Accepted: 09/19/2020] [Indexed: 06/11/2023]
Abstract
Prokaryotic Nostoc, one of the world's most conspicuous and widespread algal genera (similar to eukaryotic algae, plants, and animals) is known to support a microbiome that influences host ecological roles. Past taxonomic characterizations of surface microbiota (epimicrobiota) of free-living Nostoc sampled from freshwater systems employed 16S rRNA genes, typically amplicons. We compared taxa identified from 16S, 18S, 23S, and 28S rRNA gene sequences filtered from shotgun metagenomic sequence and used microscopy to illuminate epimicrobiota diversity for Nostoc sampled from a wetland in the northern Chilean Altiplano. Phylogenetic analysis and rRNA gene sequence abundance estimates indicated that the host was related to Nostoc punctiforme PCC 73102. Epimicrobiota were inferred to include 18 epicyanobacterial genera or uncultured taxa, six epieukaryotic algal genera, and 66 anoxygenic bacterial genera, all having average genomic coverage ≥90X. The epicyanobacteria Geitlerinemia, Oscillatoria, Phormidium, and an uncultured taxon were detected only by 16S rRNA gene; Gloeobacter and Pseudanabaena were detected using 16S and 23S; and Phormididesmis, Neosynechococcus, Symphothece, Aphanizomenon, Nodularia, Spirulina, Nodosilinea, Synechococcus, Cyanobium, and Anabaena (the latter corroborated by microscopy), plus two uncultured cyanobacterial taxa (JSC12, O77) were detected only by 23S rRNA gene sequences. Three chlamydomonad and two heterotrophic stramenopiles genera were inferred from 18S; the streptophyte green alga Chaetosphaeridium globosum was detected by microscopy and 28S rRNA genes, but not 18S rRNA genes. Overall, >60% of epimicrobial taxa were detected by markers other than 16S rRNA genes. Some algal taxa observed microscopically were not detected from sequence data. Results indicate that multiple taxonomic markers derived from metagenomic sequence data and microscopy increase epimicrobiota detection.
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Affiliation(s)
- Anchittha Satjarak
- Plants of Thailand Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, 103330, Thailand
| | - Linda E Graham
- Department of Botany, University of Wisconsin, Madison, Wisconsin, 53706, USA
| | | | - Marie T Trest
- Department of Botany, University of Wisconsin, Madison, Wisconsin, 53706, USA
| | - Lee W Wilcox
- Department of Botany, University of Wisconsin, Madison, Wisconsin, 53706, USA
| | - Martha E Cook
- School of Biological Sciences, Illinois State University, Normal, Illinois, 61790, USA
| | - Jennifer J Knack
- Department of Biology, University of Minnesota, Duluth, Minnesota, 55812, USA
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Dinoroseobacter shibae Outer Membrane Vesicles Are Enriched for the Chromosome Dimer Resolution Site dif. mSystems 2021; 6:6/1/e00693-20. [PMID: 33436507 PMCID: PMC7901474 DOI: 10.1128/msystems.00693-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Gram-negative bacteria continually form vesicles from their outer membrane (outer membrane vesicles [OMVs]) during normal growth. OMVs frequently contain DNA, and it is unclear how DNA can be shuffled from the cytoplasm to the OMVs. Outer membrane vesicles (OMVs) are universally produced by prokaryotes and play important roles in symbiotic and pathogenic interactions. They often contain DNA, but a mechanism for its incorporation is lacking. Here, we show that Dinoroseobacter shibae, a dinoflagellate symbiont, constitutively secretes OMVs containing DNA. Time-lapse microscopy captured instances of multiple OMV production at the septum during cell division. DNA from the vesicle lumen was up to 22-fold enriched for the region around the terminus of replication (ter). The peak of coverage was located at dif, a conserved 28-bp palindromic sequence required for binding of the site-specific tyrosine recombinases XerC/XerD. These enzymes are activated at the last stage of cell division immediately prior to septum formation when they are bound by the divisome protein FtsK. We suggest that overreplicated regions around the terminus have been repaired by the FtsK-dif-XerC/XerD molecular machinery. The vesicle proteome was clearly dominated by outer membrane and periplasmic proteins. Some of the most abundant vesicle membrane proteins were predicted to be required for direct interaction with peptidoglycan during cell division (LysM, Tol-Pal, Spol, lytic murein transglycosylase). OMVs were 15-fold enriched for the saturated fatty acid 16:00. We hypothesize that constitutive OMV secretion in D. shibae is coupled to cell division. The footprint of the FtsK-dif-XerC/XerD molecular machinery suggests a novel potentially highly conserved route for incorporation of DNA into OMVs. Clearing the division site from small DNA fragments might be an important function of vesicles produced during exponential growth under optimal conditions. IMPORTANCE Gram-negative bacteria continually form vesicles from their outer membrane (outer membrane vesicles [OMVs]) during normal growth. OMVs frequently contain DNA, and it is unclear how DNA can be shuffled from the cytoplasm to the OMVs. We studied OMV cargo in Dinoroseobacter shibae, a symbiont of dinoflagellates, using microscopy and a multi-omics approach. We found that vesicles formed during undisturbed exponential growth contain DNA which is enriched for genes around the replication terminus, specifically, the binding site for an enzyme complex that is activated at the last stage of cell division. We suggest that the enriched genes are the result of overreplication which is repaired by their excision and excretion via membrane vesicles to clear the divisome from waste DNA.
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Witthohn M, Strieth D, Eggert S, Kins S, Ulber R, Muffler K. Heterologous production of a cyanobacterial bacteriocin with potent antibacterial activity. CURRENT RESEARCH IN BIOTECHNOLOGY 2021. [DOI: 10.1016/j.crbiot.2021.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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21
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Phylogenomics reveals the basis of adaptation of Pseudorhizobium species to extreme environments and supports a taxonomic revision of the genus. Syst Appl Microbiol 2020; 44:126165. [PMID: 33360413 DOI: 10.1016/j.syapm.2020.126165] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 11/21/2022]
Abstract
The family Rhizobiaceae includes many genera of soil bacteria, often isolated for their association with plants. Herein, we investigate the genomic diversity of a group of Rhizobium species and unclassified strains isolated from atypical environments, including seawater, rock matrix or polluted soil. Based on whole-genome similarity and core genome phylogeny, we show that this group corresponds to the genus Pseudorhizobium. We thus reclassify Rhizobium halotolerans, R. marinum, R. flavum and R. endolithicum as P. halotolerans sp. nov., P. marinum comb. nov., P. flavum comb. nov. and P. endolithicum comb. nov., respectively, and show that P. pelagicum is a synonym of P. marinum. We also delineate a new chemolithoautotroph species, P. banfieldiae sp. nov., whose type strain is NT-26T (=DSM 106348T=CFBP 8663T). This genome-based classification was supported by a chemotaxonomic comparison, with increasing taxonomic resolution provided by fatty acid, protein and metabolic profiles. In addition, we used a phylogenetic approach to infer scenarios of duplication, horizontal transfer and loss for all genes in the Pseudorhizobium pangenome. We thus identify the key functions associated with the diversification of each species and higher clades, shedding light on the mechanisms of adaptation to their respective ecological niches. Respiratory proteins acquired at the origin of Pseudorhizobium were combined with clade-specific genes to enable different strategies for detoxification and nutrition in harsh, nutrient-poor environments.
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Wiegand S, Jogler M, Boedeker C, Heuer A, Peeters SH, Kallscheuer N, Jetten MSM, Kaster AK, Rohde M, Jogler C. Updates to the recently introduced family Lacipirellulaceae in the phylum Planctomycetes: isolation of strains belonging to the novel genera Aeoliella, Botrimarina, Pirellulimonas and Pseudobythopirellula and the novel species Bythopirellula polymerisocia and Posidoniimonas corsicana. Antonie Van Leeuwenhoek 2020; 113:1979-1997. [PMID: 33151460 PMCID: PMC7717034 DOI: 10.1007/s10482-020-01486-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/19/2020] [Indexed: 02/07/2023]
Abstract
Eight novel strains of the phylum Planctomycetes were isolated from different aquatic habitats. Among these habitats were the hydrothermal vent system close to Panarea Island, a public beach at Mallorca Island, the shore of Costa Brava (Spain), and three sites with brackish water in the Baltic Sea. The genome sizes of the novel strains range from 4.33 to 6.29 Mb with DNA G+C contents between 52.8 and 66.7%. All strains are mesophilic (Topt 24-30 °C) and display generation times between 17 and 94 h. All eight isolates constitute novel species of either already described or novel genera within the family Lacipirellulaceae. Two of the novel species, Posidoniimonas polymericola (type strain Pla123aT = DSM 103020T = LMG 29466T) and Bythopirellula polymerisocia (type strain Pla144T = DSM 104841T = VKM B-3442T), belong to established genera, while the other strains represent the novel genera Aeoliella gen. nov., Botrimarina gen. nov., Pirellulimonas gen. nov. and Pseudobythopirellula gen. nov. Based on our polyphasic analysis, we propose the species Aeoliella mucimassa sp. nov. (type strain Pan181T = DSM 29370T = LMG 31346T = CECT 9840T = VKM B-3426T), Botrimarina colliarenosi sp. nov. (type strain Pla108T = DSM 103355T = LMG 29803T), Botrimarina hoheduenensis sp. nov. (type strain Pla111T = DSM 103485T = STH00945T, Jena Microbial Resource Collection JMRC), Botrimarina mediterranea sp. nov. (type strain Spa11T = DSM 100745T = LMG 31350T = CECT 9852T = VKM B-3431T), Pirellulimonas nuda sp. nov. (type strain Pla175T = DSM 109594T = CECT 9871T = VKM B-3448T) and Pseudobythopirellula maris sp. nov. (type strain Mal64T = DSM 100832T = LMG 29020T).
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Affiliation(s)
- Sandra Wiegand
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | - Mareike Jogler
- Department of Microbial Interactions, Friedrich Schiller University, Jena, Germany
| | | | - Anja Heuer
- Leibniz Institute DSMZ, Brunswick, Germany
| | - Stijn H Peeters
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | | | - Mike S M Jetten
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Brunswick, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands.
- Department of Microbial Interactions, Friedrich Schiller University, Jena, Germany.
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Wiegand S, Jogler M, Boedeker C, Heuer A, Rast P, Peeters SH, Jetten MSM, Kaster AK, Rohde M, Kallscheuer N, Jogler C. Additions to the genus Gimesia: description of Gimesia alba sp. nov., Gimesia algae sp. nov., Gimesia aquarii sp. nov., Gimesia aquatilis sp. nov., Gimesia fumaroli sp. nov. and Gimesia panareensis sp. nov., isolated from aquatic habitats of the Northern Hemisphere. Antonie Van Leeuwenhoek 2020; 113:1999-2018. [PMID: 33231764 PMCID: PMC7716864 DOI: 10.1007/s10482-020-01489-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/19/2020] [Indexed: 11/29/2022]
Abstract
Thirteen novel planctomycetal strains were isolated from five different aquatic sampling locations. These comprise the hydrothermal vent system close to Panarea Island (Italy), a biofilm on the surface of kelp at Monterey Bay (CA, USA), sediment and algae on Mallorca Island (Spain) and Helgoland Island (Germany), as well as a seawater aquarium in Braunschweig, Germany. All strains were shown to belong to the genus Gimesia. Their genomes cover a size range from 7.22 to 8.29 Mb and have a G+C content between 45.1 and 53.7%. All strains are mesophilic (Topt 26-33 °C) with generation times between 12 and 32 h. Analysis of fatty acids yielded palmitic acid (16:0) and a fatty acid with the equivalent chain length of 15.817 as major compounds. While five of the novel strains belong to the already described species Gimesia maris and Gimesia chilikensis, the other strains belong to novel species, for which we propose the names Gimesia alba (type strain Pan241wT = DSM 100744T = LMG 31345T = CECT 9841T = VKM B-3430T), Gimesia algae (type strain Pan161T = CECT 30192T = STH00943T = LMG 29130T), Gimesia aquarii (type strain V144T = DSM 101710T = VKM B-3433T), Gimesia fumaroli (type strain Enr17T = DSM 100710T = VKM B-3429T) and Gimesia panareensis (type strain Enr10T = DSM 100416T = LMG 29082T). STH numbers refer to the Jena Microbial Resource Collection (JMRC).
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Affiliation(s)
- Sandra Wiegand
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Mareike Jogler
- Department of Microbial Interactions, Friedrich-Schiller-University, Jena, Germany
| | | | - Anja Heuer
- Leibniz Institute DSMZ, Brunswick, Germany
| | | | - Stijn H Peeters
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Brunswick, Germany
| | | | - Christian Jogler
- Department of Microbial Interactions, Friedrich-Schiller-University, Jena, Germany.
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands.
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Kallscheuer N, Jogler M, Wiegand S, Peeters SH, Heuer A, Boedeker C, Jetten MSM, Rohde M, Jogler C. Rubinisphaera italica sp. nov. isolated from a hydrothermal area in the Tyrrhenian Sea close to the volcanic island Panarea. Antonie Van Leeuwenhoek 2020; 113:1727-1736. [PMID: 31773447 PMCID: PMC7717053 DOI: 10.1007/s10482-019-01329-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 09/09/2019] [Indexed: 01/09/2023]
Abstract
Planctomycetes is a fascinating phylum of mostly aquatic bacteria, not only due to the environmental importance in global carbon and nitrogen cycles, but also because of a unique cell biology. Their lifestyle and metabolic capabilities are not well explored, which motivated us to study the role of Planctomycetes in biofilms on marine biotic surfaces. Here, we describe the novel strain Pan54T which was isolated from algae in a hydrothermal area close to the volcanic island Panarea in the Tyrrhenian Sea, north of Sicily in Italy. The strain grew best at pH 9.0 and 26 °C and showed typical characteristics of planctomycetal bacteria, e.g. division by polar budding, formation of aggregates and presence of stalks and crateriform structures. Phylogenetically, the strain belongs to the genus Rubinisphaera. Our analysis suggests that Pan54T represents a novel species of this genus, for which we propose the name Rubinisphaera italica sp. nov. We suggest Pan54T (= DSM 29369 = LMG 29789) as the type strain of the novel species.
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Affiliation(s)
- Nicolai Kallscheuer
- Department of Microbiology, Radboud Universiteit Nijmegen, Nijmegen, The Netherlands
| | - Mareike Jogler
- Department of Microbiology, Radboud Universiteit Nijmegen, Nijmegen, The Netherlands
- Leibniz Institute DSMZ, Braunschweig, Germany
| | - Sandra Wiegand
- Department of Microbiology, Radboud Universiteit Nijmegen, Nijmegen, The Netherlands
| | - Stijn H Peeters
- Department of Microbiology, Radboud Universiteit Nijmegen, Nijmegen, The Netherlands
| | - Anja Heuer
- Leibniz Institute DSMZ, Braunschweig, Germany
| | | | - Mike S M Jetten
- Department of Microbiology, Radboud Universiteit Nijmegen, Nijmegen, The Netherlands
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, HZI, Braunschweig, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud Universiteit Nijmegen, Nijmegen, The Netherlands.
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Synergistic biodegradation of aromatic-aliphatic copolyester plastic by a marine microbial consortium. Nat Commun 2020; 11:5790. [PMID: 33188179 PMCID: PMC7666164 DOI: 10.1038/s41467-020-19583-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/13/2020] [Indexed: 12/12/2022] Open
Abstract
The degradation of synthetic polymers by marine microorganisms is not as well understood as the degradation of plastics in soil and compost. Here, we use metagenomics, metatranscriptomics and metaproteomics to study the biodegradation of an aromatic-aliphatic copolyester blend by a marine microbial enrichment culture. The culture can use the plastic film as the sole carbon source, reaching maximum conversion to CO2 and biomass in around 15 days. The consortium degrades the polymer synergistically, with different degradation steps being performed by different community members. We identify six putative PETase-like enzymes and four putative MHETase-like enzymes, with the potential to degrade aliphatic-aromatic polymers and their degradation products, respectively. Our results show that, although there are multiple genes and organisms with the potential to perform each degradation step, only a few are active during biodegradation. The degradation of plastics by marine microbes is not well understood. Here, Meyer-Cifuentes et al. use a meta-omics approach to study the biodegradation of an aromatic-aliphatic copolyester blend by a marine microbial enrichment culture, showing that different degradation steps are performed by different microorganisms.
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26
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Moya A, Oliver JL, Verdú M, Delaye L, Arnau V, Bernaola-Galván P, de la Fuente R, Díaz W, Gómez-Martín C, González FM, Latorre A, Lebrón R, Román-Roldán R. Driven progressive evolution of genome sequence complexity in Cyanobacteria. Sci Rep 2020; 10:19073. [PMID: 33149190 PMCID: PMC7643063 DOI: 10.1038/s41598-020-76014-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023] Open
Abstract
Progressive evolution, or the tendency towards increasing complexity, is a controversial issue in biology, which resolution entails a proper measurement of complexity. Genomes are the best entities to address this challenge, as they encode the historical information of a species' biotic and environmental interactions. As a case study, we have measured genome sequence complexity in the ancient phylum Cyanobacteria. To arrive at an appropriate measure of genome sequence complexity, we have chosen metrics that do not decipher biological functionality but that show strong phylogenetic signal. Using a ridge regression of those metrics against root-to-tip distance, we detected positive trends towards higher complexity in three of them. Lastly, we applied three standard tests to detect if progressive evolution is passive or driven-the minimum, ancestor-descendant, and sub-clade tests. These results provide evidence for driven progressive evolution at the genome-level in the phylum Cyanobacteria.
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Affiliation(s)
- Andrés Moya
- Institute of Integrative Systems Biology (I2Sysbio), University of València and Consejo Superior de Investigaciones Científicas (CSIC), 46980, Valencia, Spain.
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), 46020, Valencia, Spain.
- CIBER in Epidemiology and Public Health, 28029, Madrid, Spain.
| | - José L Oliver
- Department of Genetics, Faculty of Sciences, University of Granada, 18071, Granada, Spain
- Laboratory of Bioinformatics, Institute of Biotechnology, Center of Biomedical Research, 18100, Granada, Spain
| | - Miguel Verdú
- Centro de Investigaciones sobre Desertificación, Consejo Superior de Investigaciones Científicas (CSIC), University of València and Generalitat Valenciana, 46113, Valencia, Spain
| | - Luis Delaye
- Department of Genetic Engineering, CINVESTAV, 36821, Irapuato, Mexico
| | - Vicente Arnau
- Institute of Integrative Systems Biology (I2Sysbio), University of València and Consejo Superior de Investigaciones Científicas (CSIC), 46980, Valencia, Spain
| | - Pedro Bernaola-Galván
- Department of Applied Physics II and Institute Carlos I for Theoretical and Computational Physics, University of Málaga, 29071, Málaga, Spain
| | - Rebeca de la Fuente
- Institute for Cross-Disciplinary Physics and Complex Systems (IFISC), Consejo Superior de Investigaciones Científicas (CSIC) and University of Balearic Islands, 07122, Palma de Mallorca, Spain
| | - Wladimiro Díaz
- Institute of Integrative Systems Biology (I2Sysbio), University of València and Consejo Superior de Investigaciones Científicas (CSIC), 46980, Valencia, Spain
| | - Cristina Gómez-Martín
- Department of Genetics, Faculty of Sciences, University of Granada, 18071, Granada, Spain
- Laboratory of Bioinformatics, Institute of Biotechnology, Center of Biomedical Research, 18100, Granada, Spain
| | | | - Amparo Latorre
- Institute of Integrative Systems Biology (I2Sysbio), University of València and Consejo Superior de Investigaciones Científicas (CSIC), 46980, Valencia, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), 46020, Valencia, Spain
- CIBER in Epidemiology and Public Health, 28029, Madrid, Spain
| | - Ricardo Lebrón
- Department of Genetics, Faculty of Sciences, University of Granada, 18071, Granada, Spain
- Laboratory of Bioinformatics, Institute of Biotechnology, Center of Biomedical Research, 18100, Granada, Spain
| | - Ramón Román-Roldán
- Department of Applied Physics, University of Granada, 18071, Granada, Spain
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27
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Jaiswal D, Wangikar PP. Dynamic Inventory of Intermediate Metabolites of Cyanobacteria in a Diurnal Cycle. iScience 2020; 23:101704. [PMID: 33196027 PMCID: PMC7644974 DOI: 10.1016/j.isci.2020.101704] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/15/2020] [Accepted: 10/15/2020] [Indexed: 11/25/2022] Open
Abstract
Cyanobacteria are gaining importance both as hosts for photoautotrophic production of chemicals and as model systems for studies of diurnal lifestyle. The proteome and transcriptome of cyanobacteria have been closely examined under diurnal growth, whereas the downstream effects on the intermediary metabolism have not received sufficient attention. The present study focuses on identifying the cellular metabolites whose inventories undergo dramatic changes in a fast-growing cyanobacterium, Synechococcus elongatus PCC 11801. We identified and quantified 67 polar metabolites, whose inventory changes significantly during diurnal growth, with some metabolites changing by 100-fold. The Calvin-Benson-Bassham cycle intermediates peak at midday to support fast growth. The hitherto unexplored γ-glutamyl peptides act as reservoirs of amino acids. Interestingly, several storage molecules or their precursors accumulate during the dark phase, dispelling the notion that all biosynthetic activity takes place in the light phase. Our results will guide metabolic modeling and strain engineering of cyanobacteria. We identify and quantify 67 polar intermediate metabolites in cyanobacteria via LC-MS A number of metabolites show large variations during the diurnal cycle Intermediates of the CBB cycle peak at midday, coinciding with peak in growth rate Gamma-glutamyl dipeptides identified as new storage compounds that peak at dawn
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Affiliation(s)
- Damini Jaiswal
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.,DBT-PAN IIT Centre for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.,Wadhwani Research Centre for Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Koblitz J, Schomburg D, Neumann-Schaal M. MetaboMAPS: Pathway sharing and multi-omics data visualization in metabolic context. F1000Res 2020; 9:288. [PMID: 32765840 PMCID: PMC7383707 DOI: 10.12688/f1000research.23427.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/13/2020] [Indexed: 01/08/2023] Open
Abstract
Metabolic pathways are an important part of systems biology research since they illustrate complex interactions between metabolites, enzymes, and regulators. Pathway maps are drawn to elucidate metabolism or to set data in a metabolic context. We present MetaboMAPS, a web-based platform to visualize numerical data on individual metabolic pathway maps. Metabolic maps can be stored, distributed and downloaded in SVG-format. MetaboMAPS was designed for users without computational background and supports pathway sharing without strict conventions. In addition to existing applications that established standards for well-studied pathways, MetaboMAPS offers a niche for individual, customized pathways beyond common knowledge, supporting ongoing research by creating publication-ready visualizations of experimental data.
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Affiliation(s)
- Julia Koblitz
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
- Braunschweig Integrated Centre of Systems Biology, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Dietmar Schomburg
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
- Braunschweig Integrated Centre of Systems Biology, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Meina Neumann-Schaal
- Braunschweig Integrated Centre of Systems Biology, Technische Universität Braunschweig, Braunschweig, 38106, Germany
- Leibniz-Institut DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124, Germany
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29
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Koblitz J, Schomburg D, Neumann-Schaal M. MetaboMAPS: Pathway sharing and multi-omics data visualization in metabolic context. F1000Res 2020; 9:288. [PMID: 32765840 PMCID: PMC7383707 DOI: 10.12688/f1000research.23427.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/17/2020] [Indexed: 03/30/2024] Open
Abstract
Metabolic pathways are an important part of systems biology research since they illustrate complex interactions between metabolites, enzymes, and regulators. Pathway maps are drawn to elucidate metabolism or to set data in a metabolic context. We present MetaboMAPS, a web-based platform to visualize numerical data on individual metabolic pathway maps. Metabolic maps can be stored, distributed and downloaded in SVG-format. MetaboMAPS was designed for users without computational background and supports pathway sharing without strict conventions. In addition to existing applications that established standards for well-studied pathways, MetaboMAPS offers a niche for individual, customized pathways beyond common knowledge, supporting ongoing research by creating publication-ready visualizations of experimental data.
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Affiliation(s)
- Julia Koblitz
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
- Braunschweig Integrated Centre of Systems Biology, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Dietmar Schomburg
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
- Braunschweig Integrated Centre of Systems Biology, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Meina Neumann-Schaal
- Braunschweig Integrated Centre of Systems Biology, Technische Universität Braunschweig, Braunschweig, 38106, Germany
- Leibniz-Institut DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, 38124, Germany
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30
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Nelson JM, Hauser DA, Gudiño JA, Guadalupe YA, Meeks JC, Salazar Allen N, Villarreal JC, Li FW. Complete Genomes of Symbiotic Cyanobacteria Clarify the Evolution of Vanadium-Nitrogenase. Genome Biol Evol 2020; 11:1959-1964. [PMID: 31243438 PMCID: PMC6645180 DOI: 10.1093/gbe/evz137] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2019] [Indexed: 02/07/2023] Open
Abstract
Plant endosymbiosis with nitrogen-fixing cyanobacteria has independently evolved in diverse plant lineages, offering a unique window to study the evolution and genetics of plant–microbe interaction. However, very few complete genomes exist for plant cyanobionts, and therefore little is known about their genomic and functional diversity. Here, we present four complete genomes of cyanobacteria isolated from bryophytes. Nanopore long-read sequencing allowed us to obtain circular contigs for all the main chromosomes and most of the plasmids. We found that despite having a low 16S rRNA sequence divergence, the four isolates exhibit considerable genome reorganizations and variation in gene content. Furthermore, three of the four isolates possess genes encoding vanadium (V)-nitrogenase (vnf), which is uncommon among diazotrophs and has not been previously reported in plant cyanobionts. In two cases, the vnf genes were found on plasmids, implying possible plasmid-mediated horizontal gene transfers. Comparative genomic analysis of vnf-containing cyanobacteria further identified a conserved gene cluster. Many genes in this cluster have not been functionally characterized and would be promising candidates for future studies to elucidate V-nitrogenase function and regulation.
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Affiliation(s)
- Jessica M Nelson
- Boyce Thompson Institute, Ithaca, New York.,Plant Biology Section, Cornell University, Ithaca, New York
| | - Duncan A Hauser
- Boyce Thompson Institute, Ithaca, New York.,Plant Biology Section, Cornell University, Ithaca, New York
| | - José A Gudiño
- Smithsonian Tropical Research Institute, Panama City, Panama
| | | | - John C Meeks
- Department of Microbiology and Molecular Genetics, University of California, Davis, California
| | | | - Juan Carlos Villarreal
- Smithsonian Tropical Research Institute, Panama City, Panama.,Department of Biology, Laval University, Quebec City, Quebec, Canada
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, New York.,Plant Biology Section, Cornell University, Ithaca, New York
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Jaiswal D, Sengupta A, Sengupta S, Madhu S, Pakrasi HB, Wangikar PP. A Novel Cyanobacterium Synechococcus elongatus PCC 11802 has Distinct Genomic and Metabolomic Characteristics Compared to its Neighbor PCC 11801. Sci Rep 2020; 10:191. [PMID: 31932622 PMCID: PMC6957532 DOI: 10.1038/s41598-019-57051-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/20/2019] [Indexed: 11/09/2022] Open
Abstract
Cyanobacteria, a group of photosynthetic prokaryotes, are attractive hosts for biotechnological applications. It is envisaged that future biorefineries will deploy engineered cyanobacteria for the conversion of carbon dioxide to useful chemicals via light-driven, endergonic reactions. Fast-growing, genetically amenable, and stress-tolerant cyanobacteria are desirable as chassis for such applications. The recently reported strains such as Synechococcus elongatus UTEX 2973 and PCC 11801 hold promise, but additional strains may be needed for the ongoing efforts of metabolic engineering. Here, we report a novel, fast-growing, and naturally transformable cyanobacterium, S. elongatus PCC 11802, that shares 97% genome identity with its closest neighbor S. elongatus PCC 11801. The new isolate has a doubling time of 2.8 h at 1% CO2, 1000 µmole photons.m-2.s-1 and grows faster under high CO2 and temperature compared to PCC 11801 thus making it an attractive host for outdoor cultivations and eventual applications in the biorefinery. Furthermore, S. elongatus PCC 11802 shows higher levels of key intermediate metabolites suggesting that this strain might be better suited for achieving high metabolic flux in engineered pathways. Importantly, metabolite profiles suggest that the key enzymes of the Calvin cycle are not repressed under elevated CO2 in the new isolate, unlike its closest neighbor.
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Affiliation(s)
- Damini Jaiswal
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Annesha Sengupta
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Shinjinee Sengupta
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
- DBT-PAN IIT Centre for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Swati Madhu
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Himadri B Pakrasi
- Department of Biology, Washington University, St. Louis, MO, 63130, USA
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, 63130, USA
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
- DBT-PAN IIT Centre for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
- Wadhwani Research Centre for Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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32
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Three novel Rubripirellula species isolated from plastic particles submerged in the Baltic Sea and the estuary of the river Warnow in northern Germany. Antonie van Leeuwenhoek 2019; 113:1767-1778. [DOI: 10.1007/s10482-019-01368-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 11/28/2019] [Indexed: 12/25/2022]
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